Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin

Abstract

The Enteritidis and Dublin serovars of Salmonella enterica are closely related, yet they differ significantly in pathogenicity and epidemiology. S. Enteritidis is a broad host range serovar that commonly causes gastroenteritis and infrequently causes invasive disease in humans. S. Dublin mainly colonizes cattle but upon infecting humans often results in invasive disease.To gain a broader view of the extent of these differences we conducted microarray-based comparative genomics between several field isolates from each serovar. Genome degradation has been correlated with host adaptation in Salmonella, thus we also compared at whole genome scale the available genomic sequences of them to evaluate pseudogene composition within each serovar.Microarray analysis revealed 3771 CDS shared by both serovars while 33 were only present in Enteritidis and 87 were exclusive to Dublin. Pseudogene evaluation showed 177 inactive CDS in S. Dublin which correspond to active genes in S. Enteritidis, nine of which are also inactive in the host adapted S. Gallinarum and S. Choleraesuis serovars. Sequencing of these 9 CDS in several S. Dublin clinical isolates revealed that they are pseudogenes in all of them, indicating that this feature is not peculiar to the sequenced strain. Among these CDS, shdA (Peyer´s patch colonization factor) and mglA (galactoside transport ATP binding protein), appear also to be inactive in the human adapted S. Typhi and S. Paratyphi A, suggesting that functionality of these genes may be relevant for the capacity of certain Salmonella serovars to infect a broad range of hosts.

Repression of Flagella Is a Common Trait in Field Isolates of Salmonella enterica Serovar Dublin and Is Associated with Invasive Human Infections

“…We previously analyzed the SDu1 to SDu3 and SDu5 isolates by comparative genomic hybridization using a Salmonella pan-array, but no signal for tviA was detected in the genomes of these isolates (49). This indicates that a different mechanism mediates fliC repression in S. Dublin.…”

“…Indeed, we have shown by comparative genomics that S. Dublin has a larger number of pseudogenes than its close relative but ubiquitous serovar S. Enteritidis (49). Moreover, Salmonella enterica serovar Gallinarum, a serovar closely related to S. Dublin and S. Enteritidis that is avian restricted and causes an invasive typhoid-like disease in chickens, is nonflagellated due to pseudogene accumulation in flagellar genes (54).…”

Host Specificity of Bacterial Pathogens

“…The specialist Y. ruckeri has the smallest genome of any Yersinia species, although this does not appear to be a result of reductive evolution, as its genome contains relatively few pseudogenes. Both Y. pestis and Y. ruckeri lack genes for urease, vitamin B12 metabolism, and the methionine salvage pathway, perhaps because these pathogens do not colonize the mammalian intestine (Chen et al 2010) Betancor et al 2012). The pigeonassociated S. Typhimurium DT2 strain 94-213 has 84 pseudogenes, including 21 loci that are intact in other closely related S. Typhimurium strains, and shows distinctive patterns of gene expression (Kingsley et al 2013).…”

“…For example, the shdA and misL genes encode nonfimbrial adhesins that enhance intestinal colonization of S. Typhimurium (Kingsley et al 2000Dorsey et al 2005). Pseudogene formation in host-restricted Salmonella serovars has inactivated both shdA (S. Typhi, S. Paratyphi A, S. Paratyphi C, S. Dublin, and S. Gallinarum) and misL (S. Typhi) McClelland et al 2004;Thomson et al 2008;Liu et al 2009;Betancor et al 2012). Another group of intestinal colonization factors of S. Typhimurium is encoded by fimbrial operons of the chaperone usher assembly class .…”

Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo

“…It is well known that S. Dublin is highly invasive in cattle and humans when compared to other NTS [38]. In humans, S. Dublin often results in bacteraemia with severe disease and high mortality [39]. In S. Typhimurium ST313, the hypothetical virulence determinant (ST313-TD) is included within a 17.7 kb region that may represent a novel pathogenicity island (ST313-GI).…”